Image: Senior author Dr. Marija Drndic (Photo courtesy of the University of Pennsylvania).

Image: Nanopore-based analysis is a single-molecule technique that promises to carry out a range of analyses orders of magnitude faster and more economically than current methods, including length measurement, specific sequence detection, single-molecule dynamics, and ultimately de novo sequencing (Photo courtesy of the University of Pennsylvania).

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A recent paper described the development of a prototype solid-state nanopore mechanism for the easily reproducible study of the nucleotide bases comprising single DNA molecules.

While biological nanopores have recently demonstrated the ability to resolve single nucleotides within individual DNA molecules, similar developments with solid-state nanopores have lagged, due to challenges both in fabricating stable nanopores of similar dimensions as biological nanopores and in achieving sufficiently low-noise and high-bandwidth recordings. Solid-state nanopore devices, comprising thin solid-state membranes, offer advantages over their biological counterparts in that they can be more easily shipped and integrated with other electronics.

The nanopores concept involves using an applied voltage to drive charged molecules, such as DNA or proteins, through a narrow pore that separates chambers of electrolyte solution. This voltage also drives a flow of electrolyte ions through the pore, measured as an electric current. When molecules pass through the pore, they block the flow of ions, and thus their structure and length can be determined based on the degree and duration of the resulting current reductions.

Investigators at the University of Pennsylvania (Philadelphia, USA; www.upenn.edu) described in the April 26, 2013, online edition of the journal ACS Nano the preparation of small silicon nitride nanopores (0.8–2.0 nm in diameter, in 5.0–8.0 nm-thick membranes). These nanopores could resolve differences between ionic current signals produced by short (30 base) single stranded DNA homopolymers poly(adenine), poly(cytosine), and poly(thymine), when combined with measurement electronics that allowed a signal-to-noise ratio of better than 10 to be achieved at 1-MHz bandwidth.

“While biological nanopores have shown the ability to resolve single nucleotides, solid-state alternatives have lagged due to two challenges of actually manufacturing the right-sized pores and achieving high-signal, low-noise and high-bandwidth measurements,” said senior author Dr. Marija Drndić, associate professor of physics and astronomy at the University of Pennsylvania. “We are attacking those two challenges here.”

“The way we make the nanopores in silicon nitride makes them taper off, so that the effective thickness is about a third of the rest of the membrane,” said Dr. Drndić. “We show that these small pores are sensitive to the base content, and we saw these results in pores with diameters between one and two nanometers, which is actually encouraging because it suggests some manufacturing variability may be okay.”

The investigators acknowledged that identifying intramolecular DNA sequences with silicon nitride nanopores will require further improvements in nanopore sensitivity and noise levels. Nonetheless, the homopolymer differentiation described in the current study represented an important milestone in the development of solid-state nanopores.